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Avoid duplicate Zarr array read #8472

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merged 5 commits into from
Dec 1, 2023
Merged

Avoid duplicate Zarr array read #8472

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255bd20
Avoid duplicate Zarr array read
dcherian Nov 21, 2023
5b4f3c3
Update xarray/backends/zarr.py
dcherian Nov 21, 2023
c907df4
Move test over to zarrbase
dcherian Nov 21, 2023
49be9c0
cleanup ZarrArrayWrapper
dcherian Nov 21, 2023
cd53784
Merge branch 'main' into optimize-zarr-read
andersy005 Dec 1, 2023
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7 changes: 4 additions & 3 deletions xarray/backends/zarr.py
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Original file line number Diff line number Diff line change
Expand Up @@ -63,13 +63,14 @@ def encode_zarr_attr_value(value):
class ZarrArrayWrapper(BackendArray):
__slots__ = ("datastore", "dtype", "shape", "variable_name", "_array")

def __init__(self, variable_name, datastore):
def __init__(self, variable_name, zarr_array, datastore):
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Suggested change
def __init__(self, variable_name, zarr_array, datastore):
def __init__(self, zarr_array):

Fairly sure this should work.

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Test this properly. I've not had good results doing this trick on a different datastore.

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thanks for the heads up! what issues did you see?

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I'm not completely sure how the zarr backend is implemented, but in my case after xr.open_dataset() the datastore is closed and not needed anymore( until .compute()).

But in this case you're sending a reference from that store to the backendarray which will be lost once the store is closed.

I've gone the opposite way, in get_variables only the required keys are sent. Then only once the backendarray __getitem__ is triggered the arrays are loaded.

I noticed this quite quickly once I played around with the dataset and loaded some variables and if you haven't noticed it yet maybe the zarr backend does some interesting tricks to avoid the closed references.

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Yerah not sure. We do have distributed tests for reading zarr so presumably it's all OK

self.datastore = datastore
self.variable_name = variable_name

# some callers attempt to evaluate an array if an `array` property exists on the object.
# we prefix with _ to avoid this inference.
self._array = self.datastore.zarr_group[self.variable_name]

self._array = zarr_array
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self.shape = self._array.shape

# preserve vlen string object dtype (GH 7328)
Expand Down Expand Up @@ -501,7 +502,7 @@ def ds(self):
return self.zarr_group

def open_store_variable(self, name, zarr_array):
data = indexing.LazilyIndexedArray(ZarrArrayWrapper(name, self))
data = indexing.LazilyIndexedArray(ZarrArrayWrapper(name, zarr_array, self))
try_nczarr = self._mode == "r"
dimensions, attributes = _get_zarr_dims_and_attrs(
zarr_array, DIMENSION_KEY, try_nczarr
Expand Down
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